rs719871

chr10-78385678-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421324.4(ENSG00000282863):n.51-143073C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,172 control chromosomes in the GnomAD database, including 867 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (867 hom., cov: 32)
• Consequence: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

(HGNC:):

LINC00595 (HGNC:31430): (long intergenic non-protein coding RNA 595)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000421324.4	n.51-143073C>T		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.63-139652C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16075 AN: 152054 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.106

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.106 AC: 16098 AN: 152172 Hom.: 867 Cov.: 32 AF XY: 0.108 AC XY: 7998 AN XY: 74374

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0942

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.105

Alfa AF: 0.106 Hom.: 420

Bravo AF: 0.106

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.15
Dann	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs719871; hg19: chr10-80145435;